Why does the material show 'unexpected' transparency effects?
For this particular problem it seams like your shader, and image's alpha are not the problem, but rather z-fighting. When there are doubled up faces with transparency  the z-fighting will not have the characteristic black look, but rather strange transparency artifacts (much like your render).  

To fix the doubled faces, check your particle settings to see if there any duplicated leaves. If there are more particles then places to emit them, then they will get doubled up.  

Here is a cube with 8 vertices, the particle system number for both is set to 32. The only difference in the two is for cube on the right I gave the particles some randomness.